Starting phenix.real_space_refine on Sun Aug 9 09:23:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.map" model { file = "/net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kd7_62264/08_2026/9kd7_62264.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 181 5.16 5 C 20709 2.51 5 N 5766 2.21 5 O 6416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33144 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9464 Classifications: {'peptide': 1188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1135} Chain breaks: 3 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'PXZ': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="PXZ M 6 " pdbres="THR M 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'PXZ:plan-1': 1, 'PXZ:plan-2': 1, 'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 414 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 650 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 90.156 83.609 29.715 1.00 79.47 S ATOM 844 SG CYS A 110 92.034 86.826 30.303 1.00 78.04 S ATOM 1149 SG CYS A 148 89.143 86.755 27.789 1.00 71.35 S ATOM 1287 SG CYS A 167 92.385 84.952 27.013 1.00 98.50 S ATOM 515 SG CYS A 67 106.481 76.717 73.305 1.00 73.21 S ATOM 537 SG CYS A 70 105.953 80.016 75.194 1.00 72.07 S ATOM 590 SG CYS A 77 102.984 77.676 74.414 1.00 94.84 S ATOM 20123 SG CYS B1163 101.587 91.805 65.253 1.00 67.02 S ATOM 20141 SG CYS B1166 100.305 89.436 62.819 1.00 60.06 S ATOM 20266 SG CYS B1182 103.941 89.043 64.532 1.00 56.13 S ATOM 20285 SG CYS B1185 103.113 91.449 61.650 1.00 74.89 S ATOM 21264 SG CYS C 86 78.859 62.362 135.579 1.00125.62 S ATOM 21281 SG CYS C 88 80.733 60.761 132.568 1.00157.71 S ATOM 21314 SG CYS C 92 79.483 58.769 135.590 1.00110.43 S ATOM 21337 SG CYS C 95 77.096 60.270 132.895 1.00 87.45 S ATOM 29004 SG CYS I 7 39.862 38.731 19.999 1.00119.58 S ATOM 29029 SG CYS I 10 43.630 38.590 20.809 1.00108.58 S ATOM 29195 SG CYS I 29 42.014 41.978 20.016 1.00121.71 S ATOM 29219 SG CYS I 32 42.442 39.323 17.393 1.00121.34 S ATOM 29546 SG CYS I 75 12.790 43.516 55.893 1.00102.57 S ATOM 29568 SG CYS I 78 12.103 39.750 55.047 1.00 97.30 S ATOM 29784 SG CYS I 103 14.742 40.804 57.721 1.00115.57 S ATOM 29804 SG CYS I 106 15.238 41.312 54.051 1.00111.84 S ATOM 29949 SG CYS J 7 51.239 54.601 115.717 1.00 70.37 S ATOM 29972 SG CYS J 10 50.368 55.969 119.235 1.00 49.73 S ATOM 30252 SG CYS J 45 47.899 55.909 116.261 1.00 66.54 S ATOM 30258 SG CYS J 46 48.993 52.790 118.337 1.00 59.66 S ATOM 31438 SG CYS L 31 83.138 28.483 100.507 1.00101.74 S ATOM 31458 SG CYS L 34 82.827 24.751 102.041 1.00 93.80 S ATOM 31562 SG CYS L 48 86.175 26.558 101.243 1.00100.73 S ATOM 31585 SG CYS L 51 83.705 25.177 98.675 1.00104.02 S Time building chain proxies: 6.10, per 1000 atoms: 0.18 Number of scatterers: 33144 At special positions: 0 Unit cell: (159.03, 148.8, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 181 16.00 P 63 15.00 Mg 1 11.99 O 6416 8.00 N 5766 7.00 C 20709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied TRANS " DVA M 2 " - " THR M 1 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA M 2 " pdb=" CB DVA M 8 " Number of C-beta restraints generated: 7518 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 49 sheets defined 39.2% alpha, 19.9% beta 22 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.664A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.762A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.738A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.081A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.170A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.513A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.806A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 4.170A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 4.133A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 4.641A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.634A pdb=" N ILE A1327 " --> pdb=" O PRO A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.629A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.902A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.571A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.606A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.555A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.577A pdb=" N TYR B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.651A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.237A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 4.510A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 4.053A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.554A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.083A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.664A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.291A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.840A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 removed outlier: 4.160A pdb=" N CYS C 86 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.535A pdb=" N CYS C 95 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 96' Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.874A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'E' and resid 3 through 27 removed outlier: 3.561A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.792A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.601A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.646A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.512A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.016A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.897A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.673A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.884A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.664A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 6.105A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.392A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.020A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.588A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.923A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.965A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB8, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.795A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.795A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.787A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.951A pdb=" N ALA B 704 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.444A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.676A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.676A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS L 58 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.772A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD4, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD5, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.542A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.548A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.639A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.379A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.540A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE7, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.518A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 Processing sheet with id=AE9, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.786A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE G 109 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS G 158 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF2, first strand: chain 'I' and resid 14 through 17 Processing sheet with id=AF3, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF4, first strand: chain 'K' and resid 19 through 23 1438 hydrogen bonds defined for protein. 3945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 9.62 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5564 1.32 - 1.44: 8720 1.44 - 1.57: 19166 1.57 - 1.70: 122 1.70 - 1.82: 290 Bond restraints: 33862 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.541 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C1 PXZ M 6 " pdb=" C2 PXZ M 6 " ideal model delta sigma weight residual 1.372 1.520 -0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" CA LYS B 471 " pdb=" C LYS B 471 " ideal model delta sigma weight residual 1.528 1.449 0.079 1.11e-02 8.12e+03 5.07e+01 bond pdb=" C2 PXZ M 6 " pdb=" N2 PXZ M 6 " ideal model delta sigma weight residual 1.344 1.468 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C11 PXZ M 6 " pdb=" N10 PXZ M 6 " ideal model delta sigma weight residual 1.297 1.419 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 33857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 45501 2.45 - 4.91: 453 4.91 - 7.36: 34 7.36 - 9.82: 4 9.82 - 12.27: 3 Bond angle restraints: 45995 Sorted by residual: angle pdb=" N GLY B 467 " pdb=" CA GLY B 467 " pdb=" C GLY B 467 " ideal model delta sigma weight residual 111.66 100.49 11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" C HIS A1387 " pdb=" CA HIS A1387 " pdb=" CB HIS A1387 " ideal model delta sigma weight residual 110.72 100.57 10.15 1.77e+00 3.19e-01 3.29e+01 angle pdb=" N LYS B 471 " pdb=" CA LYS B 471 " pdb=" C LYS B 471 " ideal model delta sigma weight residual 110.65 103.67 6.98 1.26e+00 6.30e-01 3.07e+01 angle pdb=" CB ARG A 123 " pdb=" CG ARG A 123 " pdb=" CD ARG A 123 " ideal model delta sigma weight residual 111.30 123.57 -12.27 2.30e+00 1.89e-01 2.85e+01 angle pdb=" N ASN A1390 " pdb=" CA ASN A1390 " pdb=" C ASN A1390 " ideal model delta sigma weight residual 113.17 107.05 6.12 1.26e+00 6.30e-01 2.36e+01 ... (remaining 45990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 20007 33.37 - 66.74: 561 66.74 - 100.11: 41 100.11 - 133.48: 1 133.48 - 166.85: 6 Dihedral angle restraints: 20616 sinusoidal: 9002 harmonic: 11614 Sorted by residual: dihedral pdb=" CA LEU A 597 " pdb=" C LEU A 597 " pdb=" N LEU A 598 " pdb=" CA LEU A 598 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C THR B 463 " pdb=" N THR B 463 " pdb=" CA THR B 463 " pdb=" CB THR B 463 " ideal model delta harmonic sigma weight residual -122.00 -110.14 -11.86 0 2.50e+00 1.60e-01 2.25e+01 dihedral pdb=" C SAR M 4 " pdb=" N SAR M 4 " pdb=" CA SAR M 4 " pdb=" CN SAR M 4 " ideal model delta sinusoidal sigma weight residual 71.89 -85.95 157.84 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 20613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4816 0.089 - 0.178: 343 0.178 - 0.268: 12 0.268 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 5172 Sorted by residual: chirality pdb=" P DC T 18 " pdb=" OP1 DC T 18 " pdb=" OP2 DC T 18 " pdb=" O5' DC T 18 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA DVA M 8 " pdb=" N DVA M 8 " pdb=" C DVA M 8 " pdb=" CB DVA M 8 " both_signs ideal model delta sigma weight residual False -2.44 -2.19 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LYS A1102 " pdb=" N LYS A1102 " pdb=" C LYS A1102 " pdb=" CB LYS A1102 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 5169 not shown) Planarity restraints: 5745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " -0.021 2.00e-02 2.50e+03 2.75e-02 3.77e+01 pdb=" C0' PXZ M 6 " 0.008 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " 0.002 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " -0.029 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " -0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " -0.021 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " -0.010 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " -0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " 0.012 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " 0.018 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " 0.016 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " -0.014 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " 0.009 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " 0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ M 6 " 0.043 2.00e-02 2.50e+03 pdb=" C9 PXZ M 6 " 0.020 2.00e-02 2.50e+03 pdb=" N10 PXZ M 6 " -0.053 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " 0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " 0.040 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N 36 " -0.034 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" N1 DT N 36 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT N 36 " 0.005 2.00e-02 2.50e+03 pdb=" O2 DT N 36 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT N 36 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DT N 36 " -0.036 2.00e-02 2.50e+03 pdb=" O4 DT N 36 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DT N 36 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT N 36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT N 36 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 245 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " 0.041 5.00e-02 4.00e+02 ... (remaining 5742 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 199 2.49 - 3.09: 23773 3.09 - 3.70: 52535 3.70 - 4.30: 78106 4.30 - 4.90: 128300 Nonbonded interactions: 282913 Sorted by model distance: nonbonded pdb=" OP1 C P 13 " pdb="MG MG A1803 " model vdw 1.891 2.170 nonbonded pdb=" OD2 ASP B 896 " pdb=" OH TYR L 29 " model vdw 2.051 3.040 nonbonded pdb=" OD1 ASP B 936 " pdb=" OG SER B 938 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR K 77 " pdb=" O TYR K 81 " model vdw 2.163 3.040 nonbonded pdb=" OG SER C 48 " pdb=" OE1 GLN L 66 " model vdw 2.171 3.040 ... (remaining 282908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.700 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 33899 Z= 0.267 Angle : 0.643 12.271 46043 Z= 0.366 Chirality : 0.046 0.446 5172 Planarity : 0.004 0.072 5744 Dihedral : 15.296 166.851 13095 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 0.11 % Allowed : 0.26 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.13), residues: 3952 helix: 1.07 (0.14), residues: 1351 sheet: 0.07 (0.20), residues: 651 loop : 0.09 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 123 TYR 0.019 0.002 TYR B1092 PHE 0.023 0.002 PHE K 71 TRP 0.019 0.002 TRP B 31 HIS 0.008 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.27 (33862) covalent geometry : angle 0.62582 / 0.37 (45995) hydrogen bonds : bond 0.15175 / 10.46 ( 1446) hydrogen bonds : angle 6.26297 / 4.52 ( 4049) metal coordination : bond 0.00564 / 0.34 ( 32) metal coordination : angle 4.72574 / 3.06 ( 45) Misc. bond : bond 0.00572 / 0.29 ( 4) link_TRANS : bond 0.00115 / 0.06 ( 1) link_TRANS : angle 0.51220 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 852 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8395 (mm-30) REVERT: A 416 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7875 (mtm110) REVERT: A 453 MET cc_start: 0.8438 (mpp) cc_final: 0.8167 (mpp) REVERT: A 780 VAL cc_start: 0.8896 (t) cc_final: 0.8537 (m) REVERT: A 1209 MET cc_start: 0.6941 (mmm) cc_final: 0.6031 (mmt) REVERT: A 1262 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9031 (mttt) REVERT: A 1312 ASN cc_start: 0.7711 (t0) cc_final: 0.7070 (t0) REVERT: B 429 PHE cc_start: 0.7715 (t80) cc_final: 0.7459 (t80) REVERT: B 458 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7693 (mtmt) REVERT: B 561 TRP cc_start: 0.7607 (m100) cc_final: 0.7394 (m100) REVERT: B 1098 MET cc_start: 0.8893 (mtt) cc_final: 0.8630 (mtt) REVERT: D 52 LEU cc_start: 0.7553 (mp) cc_final: 0.6913 (mt) REVERT: D 123 LEU cc_start: 0.7544 (tt) cc_final: 0.7245 (mt) REVERT: E 192 ARG cc_start: 0.8115 (ptm-80) cc_final: 0.7877 (ttp80) REVERT: G 115 MET cc_start: 0.6654 (mpp) cc_final: 0.5809 (mpp) REVERT: I 87 GLN cc_start: 0.7925 (pp30) cc_final: 0.7648 (mt0) REVERT: K 53 ASP cc_start: 0.8097 (t0) cc_final: 0.7882 (t0) REVERT: K 55 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8267 (mtpt) REVERT: L 33 GLU cc_start: 0.8057 (tt0) cc_final: 0.7773 (mm-30) REVERT: L 37 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8200 (ttmm) outliers start: 4 outliers final: 3 residues processed: 855 average time/residue: 0.2569 time to fit residues: 337.9376 Evaluate side-chains 518 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 480 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 0.0270 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.4654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 92 HIS A 118 HIS A 171 GLN A 311 GLN A 435 HIS A 587 HIS A 854 ASN A1218 GLN B 350 GLN B 932 HIS B1093 GLN B1104 HIS C 102 GLN D 37 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 146 GLN D 150 ASN D 165 GLN D 173 HIS D 179 GLN G 10 ASN G 14 HIS G 122 ASN G 126 ASN G 131 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109594 restraints weight = 49175.753| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.42 r_work: 0.3276 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33899 Z= 0.139 Angle : 0.625 14.365 46043 Z= 0.320 Chirality : 0.045 0.406 5172 Planarity : 0.005 0.070 5744 Dihedral : 13.854 177.339 5100 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.51 % Allowed : 9.24 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 3952 helix: 1.17 (0.14), residues: 1373 sheet: -0.16 (0.20), residues: 640 loop : 0.18 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 904 TYR 0.032 0.002 TYR E 46 PHE 0.023 0.002 PHE I 6 TRP 0.010 0.001 TRP A1044 HIS 0.008 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (33862) covalent geometry : angle 0.60379 / 0.32 (45995) hydrogen bonds : bond 0.04567 / 3.15 ( 1446) hydrogen bonds : angle 4.93461 / 3.56 ( 4049) metal coordination : bond 0.01210 / 0.74 ( 32) metal coordination : angle 5.22118 / 3.48 ( 45) Misc. bond : bond 0.00205 / 0.09 ( 4) link_TRANS : bond 0.00021 / 0.01 ( 1) link_TRANS : angle 0.83881 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 590 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: A 117 GLU cc_start: 0.8571 (pm20) cc_final: 0.7631 (tm-30) REVERT: A 177 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 360 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 453 MET cc_start: 0.8589 (mpp) cc_final: 0.8340 (mpp) REVERT: A 708 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6504 (ptt) REVERT: A 780 VAL cc_start: 0.8959 (t) cc_final: 0.8754 (m) REVERT: A 838 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8607 (tp40) REVERT: A 1139 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: A 1209 MET cc_start: 0.6796 (mmm) cc_final: 0.5183 (mmt) REVERT: A 1262 LYS cc_start: 0.9333 (tmtt) cc_final: 0.8938 (mttt) REVERT: A 1312 ASN cc_start: 0.7815 (t0) cc_final: 0.6713 (t0) REVERT: B 424 LEU cc_start: 0.8472 (tt) cc_final: 0.8144 (tp) REVERT: B 429 PHE cc_start: 0.8058 (t80) cc_final: 0.7689 (t80) REVERT: B 458 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7869 (mttt) REVERT: B 595 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7314 (ttp80) REVERT: B 908 GLU cc_start: 0.8332 (tp30) cc_final: 0.8120 (tp30) REVERT: B 1169 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8530 (mtm) REVERT: C 94 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8072 (ttpt) REVERT: C 102 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7507 (tm130) REVERT: C 123 ASN cc_start: 0.8256 (p0) cc_final: 0.7850 (t0) REVERT: D 123 LEU cc_start: 0.7581 (tt) cc_final: 0.7242 (mt) REVERT: E 111 VAL cc_start: 0.8882 (t) cc_final: 0.8674 (t) REVERT: E 192 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8203 (ttp80) REVERT: H 4 THR cc_start: 0.8954 (p) cc_final: 0.8507 (m) REVERT: I 45 ARG cc_start: 0.7593 (tpt-90) cc_final: 0.7219 (tpp-160) REVERT: I 73 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7481 (ttm170) REVERT: I 87 GLN cc_start: 0.7873 (pp30) cc_final: 0.7266 (mt0) REVERT: K 1 MET cc_start: 0.8139 (ttp) cc_final: 0.7848 (ttp) REVERT: K 55 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8254 (mtpt) REVERT: L 33 GLU cc_start: 0.8474 (tt0) cc_final: 0.7900 (mm-30) REVERT: L 37 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8239 (ttmm) REVERT: L 47 ARG cc_start: 0.7957 (ttp-170) cc_final: 0.7255 (ttt-90) outliers start: 53 outliers final: 29 residues processed: 622 average time/residue: 0.2407 time to fit residues: 238.1857 Evaluate side-chains 523 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 488 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1145 SER Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 301 optimal weight: 0.0000 chunk 309 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 198 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A1078 GLN B 572 HIS B 592 ASN B1093 GLN C 102 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.154745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106967 restraints weight = 49421.548| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.43 r_work: 0.3242 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33899 Z= 0.171 Angle : 0.598 17.305 46043 Z= 0.305 Chirality : 0.044 0.322 5172 Planarity : 0.004 0.071 5744 Dihedral : 13.777 178.258 5099 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.79 % Allowed : 11.77 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 3952 helix: 1.16 (0.14), residues: 1376 sheet: -0.27 (0.20), residues: 646 loop : 0.19 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 52 TYR 0.027 0.001 TYR B1092 PHE 0.028 0.002 PHE I 27 TRP 0.010 0.001 TRP B 31 HIS 0.012 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (33862) covalent geometry : angle 0.57471 / 0.30 (45995) hydrogen bonds : bond 0.04283 / 2.91 ( 1446) hydrogen bonds : angle 4.79107 / 3.45 ( 4049) metal coordination : bond 0.00971 / 0.58 ( 32) metal coordination : angle 5.36098 / 3.42 ( 45) Misc. bond : bond 0.00057 / 0.03 ( 4) link_TRANS : bond 0.00024 / 0.01 ( 1) link_TRANS : angle 0.23872 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 514 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: A 179 LEU cc_start: 0.8851 (mt) cc_final: 0.8456 (mt) REVERT: A 360 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 453 MET cc_start: 0.8630 (mpp) cc_final: 0.8381 (mpp) REVERT: A 838 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8589 (tp40) REVERT: A 1139 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: A 1198 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6265 (p0) REVERT: A 1209 MET cc_start: 0.6734 (mmm) cc_final: 0.6032 (mmt) REVERT: A 1262 LYS cc_start: 0.9345 (tmtt) cc_final: 0.8918 (mttt) REVERT: A 1315 GLU cc_start: 0.8559 (mp0) cc_final: 0.8256 (mp0) REVERT: B 301 ILE cc_start: 0.8225 (mm) cc_final: 0.7989 (mm) REVERT: B 429 PHE cc_start: 0.8065 (t80) cc_final: 0.7688 (t80) REVERT: B 458 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7886 (mtmt) REVERT: B 564 GLU cc_start: 0.7526 (tt0) cc_final: 0.7154 (tt0) REVERT: B 595 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7469 (ttp80) REVERT: B 620 ARG cc_start: 0.8253 (tpp80) cc_final: 0.8046 (tpp80) REVERT: B 706 GLN cc_start: 0.8788 (pm20) cc_final: 0.8586 (pm20) REVERT: B 875 GLU cc_start: 0.8436 (pt0) cc_final: 0.8038 (pt0) REVERT: C 94 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8163 (ttpt) REVERT: C 123 ASN cc_start: 0.8238 (p0) cc_final: 0.7776 (t0) REVERT: D 57 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8194 (pp) REVERT: D 123 LEU cc_start: 0.7590 (tt) cc_final: 0.7240 (mt) REVERT: D 208 GLU cc_start: 0.7938 (tp30) cc_final: 0.7570 (tp30) REVERT: E 50 MET cc_start: 0.7595 (tmm) cc_final: 0.7177 (tmm) REVERT: E 192 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8227 (ttp80) REVERT: G 115 MET cc_start: 0.5923 (mpp) cc_final: 0.4929 (mpp) REVERT: I 24 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7240 (tpt170) REVERT: I 45 ARG cc_start: 0.7618 (tpt-90) cc_final: 0.7076 (tpp-160) REVERT: I 73 ARG cc_start: 0.7694 (ttm170) cc_final: 0.7439 (ttm170) REVERT: I 87 GLN cc_start: 0.7954 (pp30) cc_final: 0.7246 (mt0) REVERT: J 26 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7841 (tm-30) REVERT: K 1 MET cc_start: 0.8141 (ttp) cc_final: 0.7816 (ttp) REVERT: K 55 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8271 (mtpt) REVERT: L 33 GLU cc_start: 0.8503 (tt0) cc_final: 0.7914 (mm-30) REVERT: L 37 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8294 (ttmm) outliers start: 63 outliers final: 42 residues processed: 555 average time/residue: 0.2242 time to fit residues: 198.8300 Evaluate side-chains 507 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 461 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 342 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 325 optimal weight: 0.7980 chunk 319 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 306 optimal weight: 0.0970 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN B 667 GLN B1013 ASN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 150 ASN E 5 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106326 restraints weight = 49234.379| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.44 r_work: 0.3231 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33899 Z= 0.174 Angle : 0.584 14.602 46043 Z= 0.299 Chirality : 0.044 0.335 5172 Planarity : 0.004 0.070 5744 Dihedral : 13.675 178.757 5098 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.99 % Allowed : 12.80 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.13), residues: 3952 helix: 1.16 (0.14), residues: 1378 sheet: -0.35 (0.20), residues: 645 loop : 0.20 (0.15), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 879 TYR 0.014 0.001 TYR E 46 PHE 0.026 0.002 PHE E 42 TRP 0.010 0.001 TRP B 31 HIS 0.007 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (33862) covalent geometry : angle 0.56228 / 0.30 (45995) hydrogen bonds : bond 0.04051 / 2.75 ( 1446) hydrogen bonds : angle 4.71395 / 3.39 ( 4049) metal coordination : bond 0.00765 / 0.46 ( 32) metal coordination : angle 5.02651 / 3.24 ( 45) Misc. bond : bond 0.00042 / 0.02 ( 4) link_TRANS : bond 0.00024 / 0.01 ( 1) link_TRANS : angle 0.07212 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 493 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8764 (m-10) REVERT: A 104 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8434 (mt-10) REVERT: A 161 LEU cc_start: 0.9075 (mt) cc_final: 0.8817 (mt) REVERT: A 179 LEU cc_start: 0.8873 (mt) cc_final: 0.8561 (mt) REVERT: A 360 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8694 (mm-30) REVERT: A 1139 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7772 (tp30) REVERT: A 1198 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6469 (p0) REVERT: A 1209 MET cc_start: 0.6592 (mmm) cc_final: 0.5938 (mmt) REVERT: A 1262 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8921 (mttt) REVERT: A 1315 GLU cc_start: 0.8620 (mp0) cc_final: 0.8214 (mp0) REVERT: B 404 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8860 (mttp) REVERT: B 429 PHE cc_start: 0.8032 (t80) cc_final: 0.7645 (t80) REVERT: B 458 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7878 (mtmt) REVERT: B 564 GLU cc_start: 0.7554 (tt0) cc_final: 0.7144 (tt0) REVERT: B 595 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7616 (ttp80) REVERT: B 875 GLU cc_start: 0.8438 (pt0) cc_final: 0.8063 (pt0) REVERT: B 959 ASP cc_start: 0.8543 (m-30) cc_final: 0.8014 (p0) REVERT: C 123 ASN cc_start: 0.8295 (p0) cc_final: 0.7817 (t0) REVERT: D 61 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8659 (pp20) REVERT: D 123 LEU cc_start: 0.7587 (tt) cc_final: 0.7243 (mt) REVERT: D 145 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8023 (tpt) REVERT: E 50 MET cc_start: 0.7630 (tmm) cc_final: 0.7239 (tmm) REVERT: E 192 ARG cc_start: 0.8758 (ptm-80) cc_final: 0.8241 (ttp80) REVERT: G 1 MET cc_start: 0.6915 (ptp) cc_final: 0.5729 (pmm) REVERT: H 62 SER cc_start: 0.9143 (t) cc_final: 0.8888 (m) REVERT: I 24 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7246 (tpt170) REVERT: I 87 GLN cc_start: 0.7958 (pp30) cc_final: 0.7174 (mt0) REVERT: K 1 MET cc_start: 0.8190 (ttp) cc_final: 0.7894 (ttp) REVERT: L 33 GLU cc_start: 0.8489 (tt0) cc_final: 0.7943 (mm-30) REVERT: L 37 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8295 (ttmm) outliers start: 70 outliers final: 47 residues processed: 539 average time/residue: 0.2214 time to fit residues: 191.8032 Evaluate side-chains 502 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 450 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1155 SER Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 223 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 195 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 308 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 318 optimal weight: 0.0030 chunk 159 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN B 667 GLN B 951 GLN B1013 ASN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.156208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107598 restraints weight = 49172.624| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.45 r_work: 0.3254 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33899 Z= 0.130 Angle : 0.565 15.474 46043 Z= 0.289 Chirality : 0.043 0.336 5172 Planarity : 0.004 0.069 5744 Dihedral : 13.585 179.742 5097 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 1.85 % Allowed : 13.77 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.13), residues: 3952 helix: 1.20 (0.14), residues: 1379 sheet: -0.35 (0.20), residues: 638 loop : 0.21 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 45 TYR 0.018 0.001 TYR H 129 PHE 0.029 0.002 PHE B 333 TRP 0.009 0.001 TRP B 31 HIS 0.009 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (33862) covalent geometry : angle 0.54626 / 0.29 (45995) hydrogen bonds : bond 0.03774 / 2.55 ( 1446) hydrogen bonds : angle 4.62479 / 3.33 ( 4049) metal coordination : bond 0.00769 / 0.49 ( 32) metal coordination : angle 4.63314 / 2.97 ( 45) Misc. bond : bond 0.00040 / 0.02 ( 4) link_TRANS : bond 0.00037 / 0.02 ( 1) link_TRANS : angle 0.21735 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 487 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: A 104 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: A 161 LEU cc_start: 0.9079 (mt) cc_final: 0.8818 (mt) REVERT: A 360 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8685 (mm-30) REVERT: A 1139 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: A 1198 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6721 (p0) REVERT: A 1209 MET cc_start: 0.6540 (mmm) cc_final: 0.5918 (mmt) REVERT: A 1217 LYS cc_start: 0.8722 (tptt) cc_final: 0.8245 (tppt) REVERT: A 1262 LYS cc_start: 0.9353 (tmtt) cc_final: 0.8949 (mttt) REVERT: A 1315 GLU cc_start: 0.8665 (mp0) cc_final: 0.8171 (mp0) REVERT: B 103 ASN cc_start: 0.8369 (p0) cc_final: 0.8050 (p0) REVERT: B 149 TYR cc_start: 0.6799 (m-80) cc_final: 0.6296 (m-80) REVERT: B 404 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8794 (mttm) REVERT: B 429 PHE cc_start: 0.8064 (t80) cc_final: 0.7647 (t80) REVERT: B 458 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7844 (mttt) REVERT: B 531 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7312 (mt0) REVERT: B 564 GLU cc_start: 0.7539 (tt0) cc_final: 0.7100 (tt0) REVERT: B 959 ASP cc_start: 0.8522 (m-30) cc_final: 0.7994 (p0) REVERT: C 16 ASP cc_start: 0.7892 (p0) cc_final: 0.7339 (m-30) REVERT: C 123 ASN cc_start: 0.8258 (p0) cc_final: 0.7779 (t0) REVERT: D 61 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8644 (pp20) REVERT: D 71 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7752 (mmtm) REVERT: D 123 LEU cc_start: 0.7579 (tt) cc_final: 0.7236 (mt) REVERT: E 121 MET cc_start: 0.8904 (tpp) cc_final: 0.8650 (tpp) REVERT: E 192 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8222 (ttp80) REVERT: G 1 MET cc_start: 0.6898 (ptp) cc_final: 0.5875 (pmm) REVERT: G 115 MET cc_start: 0.5889 (mpp) cc_final: 0.4963 (mpp) REVERT: H 19 ARG cc_start: 0.9153 (mtp85) cc_final: 0.8937 (mtp85) REVERT: H 35 GLN cc_start: 0.7823 (mt0) cc_final: 0.7530 (mm-40) REVERT: H 62 SER cc_start: 0.9146 (t) cc_final: 0.8886 (m) REVERT: I 24 ARG cc_start: 0.7778 (tpt90) cc_final: 0.7192 (tpt170) REVERT: I 87 GLN cc_start: 0.7935 (pp30) cc_final: 0.7267 (mm-40) REVERT: J 26 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7791 (tm-30) REVERT: K 1 MET cc_start: 0.8242 (ttp) cc_final: 0.7952 (ttp) REVERT: L 33 GLU cc_start: 0.8410 (tt0) cc_final: 0.7746 (mm-30) REVERT: L 37 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8257 (ttmm) outliers start: 65 outliers final: 43 residues processed: 532 average time/residue: 0.2128 time to fit residues: 181.7128 Evaluate side-chains 497 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 168 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 244 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 chunk 208 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN B 592 ASN B1093 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108394 restraints weight = 49141.649| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.45 r_work: 0.3256 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33899 Z= 0.121 Angle : 0.552 13.143 46043 Z= 0.282 Chirality : 0.042 0.336 5172 Planarity : 0.004 0.069 5744 Dihedral : 13.499 179.409 5097 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3952 helix: 1.28 (0.14), residues: 1381 sheet: -0.28 (0.20), residues: 644 loop : 0.23 (0.15), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 45 TYR 0.012 0.001 TYR J 21 PHE 0.039 0.001 PHE B 333 TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (33862) covalent geometry : angle 0.53525 / 0.28 (45995) hydrogen bonds : bond 0.03615 / 2.45 ( 1446) hydrogen bonds : angle 4.52927 / 3.25 ( 4049) metal coordination : bond 0.00716 / 0.45 ( 32) metal coordination : angle 4.37808 / 2.79 ( 45) Misc. bond : bond 0.00048 / 0.02 ( 4) link_TRANS : bond 0.00048 / 0.03 ( 1) link_TRANS : angle 0.40062 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 486 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: A 104 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8471 (mt-10) REVERT: A 161 LEU cc_start: 0.9089 (mt) cc_final: 0.8817 (mt) REVERT: A 360 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 801 GLU cc_start: 0.8701 (pm20) cc_final: 0.8337 (pm20) REVERT: A 930 ASP cc_start: 0.8003 (m-30) cc_final: 0.7798 (m-30) REVERT: A 1209 MET cc_start: 0.6467 (mmm) cc_final: 0.5861 (mmt) REVERT: A 1217 LYS cc_start: 0.8743 (tptt) cc_final: 0.8251 (tppt) REVERT: A 1284 MET cc_start: 0.8033 (mmm) cc_final: 0.7709 (mtt) REVERT: A 1315 GLU cc_start: 0.8673 (mp0) cc_final: 0.8192 (mp0) REVERT: B 103 ASN cc_start: 0.8442 (p0) cc_final: 0.8134 (p0) REVERT: B 135 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8333 (mtt-85) REVERT: B 149 TYR cc_start: 0.6867 (m-80) cc_final: 0.6411 (m-80) REVERT: B 404 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8782 (mttp) REVERT: B 429 PHE cc_start: 0.8059 (t80) cc_final: 0.7627 (t80) REVERT: B 458 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7791 (mttt) REVERT: B 531 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7301 (mt0) REVERT: B 564 GLU cc_start: 0.7493 (tt0) cc_final: 0.6952 (tt0) REVERT: B 875 GLU cc_start: 0.8276 (pt0) cc_final: 0.7843 (pm20) REVERT: B 908 GLU cc_start: 0.8221 (tp30) cc_final: 0.7815 (tp30) REVERT: B 959 ASP cc_start: 0.8518 (m-30) cc_final: 0.7994 (p0) REVERT: C 16 ASP cc_start: 0.7885 (p0) cc_final: 0.7280 (m-30) REVERT: C 123 ASN cc_start: 0.8260 (p0) cc_final: 0.7768 (t0) REVERT: D 71 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7821 (mmtm) REVERT: D 123 LEU cc_start: 0.7618 (tt) cc_final: 0.7303 (mt) REVERT: E 192 ARG cc_start: 0.8728 (ptm-80) cc_final: 0.8227 (ttp80) REVERT: F 103 MET cc_start: 0.8477 (mtp) cc_final: 0.8219 (mtp) REVERT: F 114 GLU cc_start: 0.8324 (tt0) cc_final: 0.8116 (tt0) REVERT: G 1 MET cc_start: 0.6700 (ptp) cc_final: 0.5852 (pmm) REVERT: G 115 MET cc_start: 0.6004 (mpp) cc_final: 0.4953 (mpp) REVERT: H 19 ARG cc_start: 0.9204 (mtp85) cc_final: 0.8998 (mtp85) REVERT: H 35 GLN cc_start: 0.7853 (mt0) cc_final: 0.7558 (mm-40) REVERT: H 62 SER cc_start: 0.9153 (t) cc_final: 0.8919 (m) REVERT: I 24 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7404 (tpt170) REVERT: I 87 GLN cc_start: 0.7938 (pp30) cc_final: 0.7250 (mm-40) REVERT: K 1 MET cc_start: 0.8193 (ttp) cc_final: 0.7943 (ttp) REVERT: K 36 GLU cc_start: 0.8215 (mp0) cc_final: 0.7777 (mp0) REVERT: K 51 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8350 (mp) REVERT: L 33 GLU cc_start: 0.8449 (tt0) cc_final: 0.7778 (mm-30) REVERT: L 37 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8307 (ttmm) outliers start: 71 outliers final: 45 residues processed: 534 average time/residue: 0.2190 time to fit residues: 188.0916 Evaluate side-chains 494 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 446 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1155 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 344 optimal weight: 50.0000 chunk 220 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN B1093 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104654 restraints weight = 49028.272| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.40 r_work: 0.3190 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33899 Z= 0.187 Angle : 0.595 15.478 46043 Z= 0.302 Chirality : 0.044 0.333 5172 Planarity : 0.004 0.070 5744 Dihedral : 13.463 179.889 5097 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 2.13 % Allowed : 14.87 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 3952 helix: 1.21 (0.14), residues: 1378 sheet: -0.37 (0.19), residues: 658 loop : 0.20 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.018 0.001 TYR H 129 PHE 0.028 0.002 PHE E 42 TRP 0.011 0.001 TRP B 31 HIS 0.009 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (33862) covalent geometry : angle 0.57635 / 0.30 (45995) hydrogen bonds : bond 0.03868 / 2.62 ( 1446) hydrogen bonds : angle 4.61670 / 3.32 ( 4049) metal coordination : bond 0.00777 / 0.45 ( 32) metal coordination : angle 4.72388 / 2.96 ( 45) Misc. bond : bond 0.00064 / 0.03 ( 4) link_TRANS : bond 0.00064 / 0.03 ( 1) link_TRANS : angle 0.54946 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 471 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8961 (mmm) cc_final: 0.8604 (tpp) REVERT: A 104 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: A 161 LEU cc_start: 0.9079 (mt) cc_final: 0.8832 (mt) REVERT: A 360 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8680 (mm-30) REVERT: A 801 GLU cc_start: 0.8748 (pm20) cc_final: 0.8444 (pm20) REVERT: A 930 ASP cc_start: 0.7972 (m-30) cc_final: 0.7744 (m-30) REVERT: A 1202 MET cc_start: 0.7032 (tpp) cc_final: 0.6820 (tpp) REVERT: A 1209 MET cc_start: 0.6486 (mmm) cc_final: 0.5815 (mmt) REVERT: A 1217 LYS cc_start: 0.8763 (tptt) cc_final: 0.8245 (tppt) REVERT: A 1284 MET cc_start: 0.8050 (mmm) cc_final: 0.7830 (mtt) REVERT: A 1315 GLU cc_start: 0.8701 (mp0) cc_final: 0.8208 (mp0) REVERT: B 103 ASN cc_start: 0.8411 (p0) cc_final: 0.8118 (p0) REVERT: B 135 ARG cc_start: 0.8586 (mtt-85) cc_final: 0.8211 (mtt-85) REVERT: B 149 TYR cc_start: 0.6900 (m-80) cc_final: 0.6475 (m-80) REVERT: B 227 LYS cc_start: 0.8471 (mttm) cc_final: 0.8205 (tttp) REVERT: B 404 LYS cc_start: 0.9173 (mmtt) cc_final: 0.8759 (mttp) REVERT: B 429 PHE cc_start: 0.8033 (t80) cc_final: 0.7600 (t80) REVERT: B 458 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7795 (mttt) REVERT: B 564 GLU cc_start: 0.7466 (tt0) cc_final: 0.6984 (tt0) REVERT: B 875 GLU cc_start: 0.8334 (pt0) cc_final: 0.7878 (pm20) REVERT: B 908 GLU cc_start: 0.8344 (tp30) cc_final: 0.7947 (tp30) REVERT: B 959 ASP cc_start: 0.8567 (m-30) cc_final: 0.7983 (p0) REVERT: C 123 ASN cc_start: 0.8366 (p0) cc_final: 0.7924 (t0) REVERT: D 52 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6673 (mm) REVERT: D 71 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7863 (mmtm) REVERT: D 123 LEU cc_start: 0.7604 (tt) cc_final: 0.7277 (mt) REVERT: E 109 ILE cc_start: 0.9176 (mt) cc_final: 0.8951 (mt) REVERT: E 192 ARG cc_start: 0.8765 (ptm-80) cc_final: 0.8234 (ttp80) REVERT: F 103 MET cc_start: 0.8573 (mtp) cc_final: 0.8263 (mtt) REVERT: G 1 MET cc_start: 0.6502 (ptp) cc_final: 0.5735 (pmm) REVERT: G 115 MET cc_start: 0.5915 (mpp) cc_final: 0.5229 (mpp) REVERT: H 19 ARG cc_start: 0.9204 (mtp85) cc_final: 0.8997 (mtp85) REVERT: H 35 GLN cc_start: 0.7921 (mt0) cc_final: 0.7636 (mm-40) REVERT: H 62 SER cc_start: 0.9171 (t) cc_final: 0.8915 (m) REVERT: I 24 ARG cc_start: 0.7772 (tpt90) cc_final: 0.7395 (tpt170) REVERT: I 87 GLN cc_start: 0.7945 (pp30) cc_final: 0.7142 (mt0) REVERT: J 26 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7887 (tm-30) REVERT: K 1 MET cc_start: 0.8258 (ttp) cc_final: 0.7970 (ttp) REVERT: K 51 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8366 (mp) REVERT: L 33 GLU cc_start: 0.8418 (tt0) cc_final: 0.7849 (mm-30) REVERT: L 37 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8350 (ttmm) REVERT: L 62 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8643 (mmmm) outliers start: 75 outliers final: 57 residues processed: 521 average time/residue: 0.2272 time to fit residues: 189.4182 Evaluate side-chains 514 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 454 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1329 THR Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1155 SER Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain B residue 1186 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain K residue 5 ASP Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 243 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 225 optimal weight: 0.2980 chunk 252 optimal weight: 0.9980 chunk 161 optimal weight: 0.0010 chunk 354 optimal weight: 6.9990 chunk 373 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A 854 ASN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.153826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105892 restraints weight = 48986.318| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.46 r_work: 0.3213 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33899 Z= 0.134 Angle : 0.571 14.079 46043 Z= 0.289 Chirality : 0.043 0.334 5172 Planarity : 0.004 0.069 5744 Dihedral : 13.429 179.460 5097 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.81 % Favored : 97.17 % Rotamer: Outliers : 1.96 % Allowed : 15.56 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3952 helix: 1.26 (0.14), residues: 1384 sheet: -0.31 (0.19), residues: 647 loop : 0.20 (0.15), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B1094 TYR 0.016 0.001 TYR A 383 PHE 0.032 0.001 PHE D 154 TRP 0.016 0.001 TRP A1228 HIS 0.004 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (33862) covalent geometry : angle 0.55448 / 0.29 (45995) hydrogen bonds : bond 0.03646 / 2.47 ( 1446) hydrogen bonds : angle 4.54040 / 3.26 ( 4049) metal coordination : bond 0.00698 / 0.41 ( 32) metal coordination : angle 4.45474 / 2.81 ( 45) Misc. bond : bond 0.00063 / 0.03 ( 4) link_TRANS : bond 0.00068 / 0.04 ( 1) link_TRANS : angle 0.40907 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 476 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8966 (mmm) cc_final: 0.8624 (tpp) REVERT: A 104 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: A 161 LEU cc_start: 0.9081 (mt) cc_final: 0.8824 (mt) REVERT: A 320 ARG cc_start: 0.8364 (ptt-90) cc_final: 0.8097 (mtm110) REVERT: A 360 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8657 (mm-30) REVERT: A 801 GLU cc_start: 0.8720 (pm20) cc_final: 0.8316 (pm20) REVERT: A 1209 MET cc_start: 0.6397 (mmm) cc_final: 0.5774 (mmt) REVERT: A 1217 LYS cc_start: 0.8763 (tptt) cc_final: 0.8250 (tppt) REVERT: A 1284 MET cc_start: 0.8093 (mmm) cc_final: 0.7880 (mtt) REVERT: A 1315 GLU cc_start: 0.8705 (mp0) cc_final: 0.8210 (mp0) REVERT: B 103 ASN cc_start: 0.8420 (p0) cc_final: 0.8121 (p0) REVERT: B 135 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: B 149 TYR cc_start: 0.6912 (m-80) cc_final: 0.6469 (m-80) REVERT: B 227 LYS cc_start: 0.8464 (mttm) cc_final: 0.8200 (tttp) REVERT: B 241 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7936 (ttm110) REVERT: B 404 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8806 (mttm) REVERT: B 429 PHE cc_start: 0.8054 (t80) cc_final: 0.7612 (t80) REVERT: B 458 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7793 (mttt) REVERT: B 531 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7403 (mt0) REVERT: B 564 GLU cc_start: 0.7423 (tt0) cc_final: 0.7038 (tt0) REVERT: B 687 GLU cc_start: 0.8133 (tt0) cc_final: 0.7658 (pt0) REVERT: B 875 GLU cc_start: 0.8288 (pt0) cc_final: 0.7885 (pm20) REVERT: B 908 GLU cc_start: 0.8270 (tp30) cc_final: 0.7902 (tp30) REVERT: B 959 ASP cc_start: 0.8557 (m-30) cc_final: 0.7977 (p0) REVERT: B 1082 MET cc_start: 0.8987 (tpp) cc_final: 0.8718 (tpp) REVERT: C 123 ASN cc_start: 0.8357 (p0) cc_final: 0.7913 (t0) REVERT: D 52 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6608 (mm) REVERT: D 71 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7894 (mmtm) REVERT: D 123 LEU cc_start: 0.7610 (tt) cc_final: 0.7273 (mt) REVERT: D 145 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.8013 (tpt) REVERT: E 109 ILE cc_start: 0.9155 (mt) cc_final: 0.8937 (mp) REVERT: E 192 ARG cc_start: 0.8720 (ptm-80) cc_final: 0.8202 (ttp80) REVERT: F 103 MET cc_start: 0.8540 (mtp) cc_final: 0.8243 (mtt) REVERT: G 1 MET cc_start: 0.6423 (ptp) cc_final: 0.5664 (pmm) REVERT: G 57 GLN cc_start: 0.8433 (mm110) cc_final: 0.8115 (mm110) REVERT: G 77 VAL cc_start: 0.8609 (p) cc_final: 0.8395 (m) REVERT: G 115 MET cc_start: 0.5925 (mpp) cc_final: 0.5273 (mpp) REVERT: H 19 ARG cc_start: 0.9196 (mtp85) cc_final: 0.8989 (mtp85) REVERT: H 35 GLN cc_start: 0.7937 (mt0) cc_final: 0.7656 (mm-40) REVERT: H 62 SER cc_start: 0.9171 (t) cc_final: 0.8917 (m) REVERT: I 24 ARG cc_start: 0.7783 (tpt90) cc_final: 0.7361 (tpt170) REVERT: I 87 GLN cc_start: 0.7931 (pp30) cc_final: 0.7250 (mm-40) REVERT: K 1 MET cc_start: 0.8250 (ttp) cc_final: 0.7956 (ttp) REVERT: K 51 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8368 (mp) REVERT: L 33 GLU cc_start: 0.8408 (tt0) cc_final: 0.7759 (mm-30) REVERT: L 37 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8336 (ttmm) outliers start: 69 outliers final: 55 residues processed: 521 average time/residue: 0.2363 time to fit residues: 197.2016 Evaluate side-chains 519 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 460 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1288 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1181 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 153 optimal weight: 0.0970 chunk 270 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 207 optimal weight: 0.0070 chunk 244 optimal weight: 0.6980 chunk 230 optimal weight: 40.0000 chunk 365 optimal weight: 0.2980 chunk 161 optimal weight: 0.7980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN K 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108138 restraints weight = 48539.351| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.40 r_work: 0.3241 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33899 Z= 0.111 Angle : 0.568 13.712 46043 Z= 0.291 Chirality : 0.042 0.333 5172 Planarity : 0.004 0.069 5744 Dihedral : 13.385 178.422 5097 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 15.81 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3952 helix: 1.28 (0.14), residues: 1397 sheet: -0.26 (0.19), residues: 650 loop : 0.22 (0.15), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1094 TYR 0.020 0.001 TYR H 129 PHE 0.037 0.001 PHE D 154 TRP 0.013 0.001 TRP A1228 HIS 0.006 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (33862) covalent geometry : angle 0.55433 / 0.29 (45995) hydrogen bonds : bond 0.03476 / 2.36 ( 1446) hydrogen bonds : angle 4.46086 / 3.20 ( 4049) metal coordination : bond 0.00624 / 0.37 ( 32) metal coordination : angle 4.05510 / 2.58 ( 45) Misc. bond : bond 0.00069 / 0.03 ( 4) link_TRANS : bond 0.00058 / 0.03 ( 1) link_TRANS : angle 0.30970 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 489 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8975 (mmm) cc_final: 0.8639 (tpp) REVERT: A 104 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: A 117 GLU cc_start: 0.8538 (pm20) cc_final: 0.7558 (tm-30) REVERT: A 161 LEU cc_start: 0.9075 (mt) cc_final: 0.8811 (mt) REVERT: A 179 LEU cc_start: 0.8860 (mt) cc_final: 0.8613 (mt) REVERT: A 216 VAL cc_start: 0.8632 (t) cc_final: 0.8411 (t) REVERT: A 360 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8606 (mm-30) REVERT: A 801 GLU cc_start: 0.8705 (pm20) cc_final: 0.8300 (pm20) REVERT: A 1209 MET cc_start: 0.6371 (mmm) cc_final: 0.5772 (mmt) REVERT: A 1217 LYS cc_start: 0.8797 (tptt) cc_final: 0.8280 (tppt) REVERT: A 1284 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: A 1315 GLU cc_start: 0.8737 (mp0) cc_final: 0.8249 (mp0) REVERT: A 1448 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: A 1454 MET cc_start: 0.5911 (pmm) cc_final: 0.5284 (pmm) REVERT: B 103 ASN cc_start: 0.8446 (p0) cc_final: 0.8149 (p0) REVERT: B 149 TYR cc_start: 0.6945 (m-80) cc_final: 0.6480 (m-80) REVERT: B 227 LYS cc_start: 0.8432 (mttm) cc_final: 0.8150 (tttp) REVERT: B 310 MET cc_start: 0.7665 (mmm) cc_final: 0.7292 (mtp) REVERT: B 404 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8713 (mttp) REVERT: B 429 PHE cc_start: 0.8027 (t80) cc_final: 0.7581 (t80) REVERT: B 458 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7694 (mttt) REVERT: B 564 GLU cc_start: 0.7436 (tt0) cc_final: 0.7082 (tt0) REVERT: B 908 GLU cc_start: 0.8215 (tp30) cc_final: 0.7846 (tp30) REVERT: B 959 ASP cc_start: 0.8556 (m-30) cc_final: 0.7995 (p0) REVERT: B 1082 MET cc_start: 0.8963 (tpp) cc_final: 0.8677 (tpp) REVERT: C 123 ASN cc_start: 0.8316 (p0) cc_final: 0.7877 (t0) REVERT: D 52 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6759 (mm) REVERT: D 71 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7905 (mmtm) REVERT: D 123 LEU cc_start: 0.7566 (tt) cc_final: 0.7238 (mt) REVERT: D 145 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (tpt) REVERT: E 192 ARG cc_start: 0.8709 (ptm-80) cc_final: 0.8300 (ttt90) REVERT: F 103 MET cc_start: 0.8495 (mtp) cc_final: 0.8219 (mtt) REVERT: G 1 MET cc_start: 0.6345 (ptp) cc_final: 0.5621 (pmm) REVERT: G 57 GLN cc_start: 0.8435 (mm110) cc_final: 0.8098 (mm110) REVERT: G 77 VAL cc_start: 0.8590 (p) cc_final: 0.8382 (m) REVERT: G 115 MET cc_start: 0.5863 (mpp) cc_final: 0.5208 (mpp) REVERT: H 19 ARG cc_start: 0.9208 (mtp85) cc_final: 0.9000 (mtp85) REVERT: H 35 GLN cc_start: 0.7936 (mt0) cc_final: 0.7678 (mm-40) REVERT: H 62 SER cc_start: 0.9168 (t) cc_final: 0.8914 (m) REVERT: I 17 ARG cc_start: 0.5919 (tpp80) cc_final: 0.4863 (mmt-90) REVERT: I 24 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7299 (tpt170) REVERT: I 87 GLN cc_start: 0.7916 (pp30) cc_final: 0.7202 (mm-40) REVERT: K 1 MET cc_start: 0.8162 (ttp) cc_final: 0.7870 (ttp) REVERT: K 36 GLU cc_start: 0.8230 (mp0) cc_final: 0.7837 (mp0) REVERT: K 51 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8298 (mp) REVERT: L 33 GLU cc_start: 0.8432 (tt0) cc_final: 0.7784 (mm-30) REVERT: L 37 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8301 (ttmm) outliers start: 62 outliers final: 42 residues processed: 529 average time/residue: 0.2200 time to fit residues: 186.3801 Evaluate side-chains 508 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 460 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 61 optimal weight: 0.9990 chunk 347 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 280 optimal weight: 0.6980 chunk 367 optimal weight: 4.9990 chunk 386 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 321 optimal weight: 4.9990 chunk 296 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN K 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106372 restraints weight = 49162.586| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.47 r_work: 0.3225 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33899 Z= 0.138 Angle : 0.574 13.283 46043 Z= 0.292 Chirality : 0.043 0.328 5172 Planarity : 0.004 0.070 5744 Dihedral : 13.361 178.439 5097 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 1.48 % Allowed : 16.30 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3952 helix: 1.26 (0.14), residues: 1404 sheet: -0.27 (0.19), residues: 645 loop : 0.24 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 47 TYR 0.013 0.001 TYR J 21 PHE 0.029 0.001 PHE E 42 TRP 0.012 0.001 TRP E 79 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (33862) covalent geometry : angle 0.55887 / 0.29 (45995) hydrogen bonds : bond 0.03539 / 2.40 ( 1446) hydrogen bonds : angle 4.45213 / 3.20 ( 4049) metal coordination : bond 0.00655 / 0.38 ( 32) metal coordination : angle 4.16977 / 2.62 ( 45) Misc. bond : bond 0.00070 / 0.03 ( 4) link_TRANS : bond 0.00066 / 0.03 ( 1) link_TRANS : angle 0.38138 / 0.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7904 Ramachandran restraints generated. 3952 Oldfield, 0 Emsley, 3952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 475 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8963 (mmm) cc_final: 0.8563 (tpp) REVERT: A 104 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (mt-10) REVERT: A 117 GLU cc_start: 0.8567 (pm20) cc_final: 0.7499 (tm-30) REVERT: A 161 LEU cc_start: 0.9078 (mt) cc_final: 0.8828 (mt) REVERT: A 179 LEU cc_start: 0.8866 (mt) cc_final: 0.8632 (mt) REVERT: A 216 VAL cc_start: 0.8640 (t) cc_final: 0.8394 (t) REVERT: A 320 ARG cc_start: 0.8277 (ptt-90) cc_final: 0.7855 (mtm110) REVERT: A 360 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8637 (mm-30) REVERT: A 801 GLU cc_start: 0.8713 (pm20) cc_final: 0.8300 (pm20) REVERT: A 1209 MET cc_start: 0.6392 (mmm) cc_final: 0.5807 (mmt) REVERT: A 1217 LYS cc_start: 0.8796 (tptt) cc_final: 0.8265 (tppt) REVERT: A 1315 GLU cc_start: 0.8745 (mp0) cc_final: 0.8258 (mp0) REVERT: A 1448 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: A 1454 MET cc_start: 0.5835 (pmm) cc_final: 0.5192 (pmm) REVERT: B 103 ASN cc_start: 0.8450 (p0) cc_final: 0.8155 (p0) REVERT: B 135 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8268 (mtt-85) REVERT: B 149 TYR cc_start: 0.7036 (m-80) cc_final: 0.6598 (m-80) REVERT: B 227 LYS cc_start: 0.8480 (mttm) cc_final: 0.8201 (tttp) REVERT: B 241 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7937 (ttm110) REVERT: B 404 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8802 (mttp) REVERT: B 429 PHE cc_start: 0.8046 (t80) cc_final: 0.7602 (t80) REVERT: B 458 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7696 (mttt) REVERT: B 531 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7062 (mt0) REVERT: B 564 GLU cc_start: 0.7431 (tt0) cc_final: 0.7114 (tt0) REVERT: B 908 GLU cc_start: 0.8239 (tp30) cc_final: 0.7867 (tp30) REVERT: B 959 ASP cc_start: 0.8584 (m-30) cc_final: 0.8009 (p0) REVERT: B 1082 MET cc_start: 0.8995 (tpp) cc_final: 0.8725 (tpp) REVERT: C 123 ASN cc_start: 0.8354 (p0) cc_final: 0.7907 (t0) REVERT: D 71 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7956 (mmtm) REVERT: D 123 LEU cc_start: 0.7568 (tt) cc_final: 0.7234 (mt) REVERT: D 145 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.8009 (tpt) REVERT: E 192 ARG cc_start: 0.8719 (ptm-80) cc_final: 0.8314 (ttt90) REVERT: F 103 MET cc_start: 0.8538 (mtp) cc_final: 0.8275 (mtt) REVERT: G 1 MET cc_start: 0.6201 (ptp) cc_final: 0.5470 (pmm) REVERT: G 57 GLN cc_start: 0.8450 (mm110) cc_final: 0.8113 (mm110) REVERT: G 77 VAL cc_start: 0.8610 (p) cc_final: 0.8387 (m) REVERT: G 115 MET cc_start: 0.5839 (mpp) cc_final: 0.5186 (mpp) REVERT: H 35 GLN cc_start: 0.7960 (mt0) cc_final: 0.7726 (mm-40) REVERT: H 62 SER cc_start: 0.9181 (t) cc_final: 0.8933 (m) REVERT: I 24 ARG cc_start: 0.7777 (tpt90) cc_final: 0.7324 (tpt170) REVERT: I 87 GLN cc_start: 0.7934 (pp30) cc_final: 0.7220 (mm-40) REVERT: K 1 MET cc_start: 0.8204 (ttp) cc_final: 0.7920 (ttp) REVERT: K 36 GLU cc_start: 0.8236 (mp0) cc_final: 0.7887 (mp0) REVERT: K 51 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8325 (mp) REVERT: L 33 GLU cc_start: 0.8427 (tt0) cc_final: 0.7786 (mm-30) REVERT: L 37 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8303 (ttmm) REVERT: L 62 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8548 (mmmm) outliers start: 52 outliers final: 42 residues processed: 509 average time/residue: 0.2227 time to fit residues: 181.9795 Evaluate side-chains 511 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 465 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1198 ASP Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 106 CYS Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 308 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A1059 HIS ** B1025 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN K 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.155111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106693 restraints weight = 48903.016| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.40 r_work: 0.3229 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33899 Z= 0.138 Angle : 0.575 13.005 46043 Z= 0.294 Chirality : 0.043 0.326 5172 Planarity : 0.004 0.070 5744 Dihedral : 13.355 178.315 5097 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 1.48 % Allowed : 16.44 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3952 helix: 1.25 (0.14), residues: 1405 sheet: -0.29 (0.19), residues: 651 loop : 0.26 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 47 TYR 0.018 0.001 TYR H 129 PHE 0.029 0.001 PHE E 42 TRP 0.010 0.001 TRP B 31 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (33862) covalent geometry : angle 0.56075 / 0.29 (45995) hydrogen bonds : bond 0.03536 / 2.40 ( 1446) hydrogen bonds : angle 4.44417 / 3.19 ( 4049) metal coordination : bond 0.00641 / 0.37 ( 32) metal coordination : angle 4.17654 / 2.62 ( 45) Misc. bond : bond 0.00074 / 0.04 ( 4) link_TRANS : bond 0.00077 / 0.04 ( 1) link_TRANS : angle 0.29677 / 0.15 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11169.27 seconds wall clock time: 191 minutes 10.27 seconds (11470.27 seconds total)